BN1902 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 4.2255e-05 1.9656e-03
Layer 2 8.5332e-05 5.2695e-03
Layer 3 1.3441e-04 8.3690e-03
Layer 6 2.0385e-04 4.0521e-02
Layer 5 4.1839e-04 2.9501e-03
Layer 1 2.0257e-02 1.7905e-01
WM 9.9957e-01 4.1141e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
ENO2 Expression Distribution
Gene Specificity Score (GSS)
ENO2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
ENO2 Layer 5 2.4883 0.7698
FAIM2 Layer 4 2.8311 0.7679
EEF1A2 Layer 5 2.5723 0.7668
ATP5F1B Layer 4 2.3496 0.7637
PPP2R1A Layer 5 2.4727 0.7576
COX6C Layer 2 2.3086 0.7509
UCHL1 Layer 5 2.3867 0.7504
SERPINI1 Layer 4 2.4609 0.7477
STXBP1 Layer 4 2.8184 0.7471
NDUFS5 Layer 4 2.5449 0.7467
ATP6V0C Layer 4 2.5928 0.7463
RAB6B Layer 4 2.3184 0.7460
CFL1 Layer 5 2.3750 0.7457
TSC22D1 Layer 4 2.6602 0.7441
NDUFA3 Layer 4 2.5215 0.7437
SYN2 Layer 5 2.8223 0.7428
PREPL Layer 4 2.2422 0.7426
NDFIP1 Layer 4 2.3213 0.7423
RTN3 Layer 2 2.3555 0.7422
SLC22A17 Layer 4 2.1152 0.7421
PRKAR1B Layer 5 2.3867 0.7414
MTCH1 Layer 4 2.4512 0.7405
CALM3 Layer 4 2.4180 0.7402
PRNP Layer 2 2.4844 0.7397
OAZ1 Layer 4 2.3154 0.7388
SKP1 Layer 4 2.3926 0.7382
GRIN1 Layer 4 2.5605 0.7381
ATP2B2 Layer 4 2.1348 0.7376
SNRPN Layer 4 2.3652 0.7373
GPX4 Layer 5 2.3555 0.7370
YPEL3 Layer 5 2.1621 0.7370
SIRPA Layer 4 2.3320 0.7367
SYN1 Layer 5 2.2773 0.7366
STMN1 Layer 4 2.5898 0.7365
KIF1A Layer 4 2.5176 0.7360
DPYSL2 Layer 5 2.4453 0.7357
NSF Layer 4 2.3896 0.7353
TPI1 Layer 5 2.5117 0.7350
YWHAH Layer 2 2.6895 0.7348
DNM1 Layer 4 2.5273 0.7342
SARAF Layer 2 2.4727 0.7339
ATP5MPL Layer 2 2.2363 0.7338
MEF2C Layer 4 2.8516 0.7335
TAGLN3 Layer 4 2.2070 0.7333
ATP9A Layer 4 2.2520 0.7332
ATP6V0A1 Layer 4 2.3555 0.7332
MORF4L1 Layer 5 2.6016 0.7331
DNAJC6 Layer 4 2.5693 0.7326
ARPP19 Layer 2 2.5117 0.7320
GDI1 Layer 4 2.3623 0.7310

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1902
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1902_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1902/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1902/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1902/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1902/report/PD/BN1902_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1902/report/PD/BN1902_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:30:42
  • Number of Processes: 10
  • Spending Time: 0h 4m